Summary In order to generate new mechanistic hypotheses on neuroHIV pathogenesis and disease progression to identify novel therapeutic targets to improve neuropsychological functioning in people with HIV, substance abuse comorbidity and neurodegenerative diseases, this proposal will utilize convergent state-of-the-art Omics strategies including transcriptomic, epitranscriptomic and proteomics. Specifically, we will carry out gene expression profiles by RNA-Seq from the frontal cortex of HIV+ patients and controls representative of cART era clinical presentations with and without histories of dependent substance abuse from samples of the National NeuroAIDS Tissue Consortium (NNTC). We will bring to bear a systems biology framework to generate mechanistic hypotheses that in preliminary studies allowed us to identify candidate drivers of gene expression changes associated with neuroHIV and neurodegenerative diseases including Alzheimer?s and Huntington?s diseases. The scientific literature together with our preliminary results, indicate that N6- methyladenosine (m6A) RNA methylation represents an additional layer of host gene expression of great potential pathogenic significance in both neuroHIV and Alzheimer?s disease. In particular, preliminary results indicate that HIV induces altered m6A methylation of transcripts involved in pathways related to synaptodendritic injury and neurodegeneration, inflammation and RNA processing, thus m6A RNA methylation profiling will also be carried out. Excessive production of the signaling molecule nitric oxide (NO) leads to protein S-nitrosylation, a posttranslational modification associated with aging, neurodegenerative diseases, including Alzheimer?s and Parkinson?s diseases, and neuroHIV. Our preliminary data show convergent results from analyses of gene expression and S-nitrosoproteomics. Therefore, we will integrate the transcriptomics with Mass Spectrometry (MS) proteomic analysis of the S-nitrosoproteome. In summary, these studies will apply an integrated Omics approach including little understood and emerging aspects of host-HIV regulatory interactions, such as RNA-methylation and protein nitrosylation in a systems biology framework to generate mechanistic hypotheses that will be tested in the second part of the grant to identify novel therapeutic concepts to improve neuropsychological functioning in people with HIV, substance abuse comorbidity and neurodegenerative diseases.